Variant report

Variant	rs909053
Chromosome Location	chr12:121237668-121237669
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:121233943..121235846-chr12:121237594..121239607,2	K562	blood:

Extended variants
information (count: 83 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10774572	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10849791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849807	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs11065264	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11065283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11065284	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11065292	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11065293	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11065300	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs11065311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11065324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1151849	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1151862	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11608262	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11611087	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1177585	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12371178	0.81[AMR][1000 genomes]
rs12579868	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12580949	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes]
rs12809299	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12822123	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs12824150	0.85[CEU][hapmap]
rs12825746	0.83[ASN][1000 genomes]
rs12831094	0.82[AMR][1000 genomes]
rs13746	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1467283	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1542859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1696357	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2015462	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2047568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2062507	0.85[CEU][hapmap]
rs2393717	0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2893876	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3213566	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3213567	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3213570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3213572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34076777	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35706672	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3809313	0.84[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3842985	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3861797	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3883901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3897746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3901854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4454799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs471688	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4766979	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4766980	0.81[AMR][1000 genomes]
rs4767935	0.85[CEU][hapmap]
rs4767937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs494632	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs508595	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs520753	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs525425	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs531782	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs534415	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs572016	0.82[ASN][1000 genomes]
rs577961	0.82[ASN][1000 genomes]
rs580240	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58291418	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs590625	0.82[ASN][1000 genomes]
rs608394	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs610694	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs618482	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs624216	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs625228	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs661647	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs668622	0.95[ASN][1000 genomes]
rs7137504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7305849	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73413868	0.81[AMR][1000 genomes]
rs7969140	0.81[AMR][1000 genomes]
rs869781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9431	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs989986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs989987	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv560438	chr12:121194565-121352206	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv1801139	chr12:121228410-121241933	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1045178	chr12:121231461-121271734	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs909053	UNQ1887	Cis_1M	lymphoblastoid	RTeQTL
rs909053	SPPL3	cis	Nerve Tibial	GTEx
rs909053	SPPL3	cis	Adipose Subcutaneous	GTEx
rs909053	ACADS	cis	Thyroid	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121206200-121238600	Weak transcription	Small Intestine	intestine
2	chr12:121211400-121260800	Weak transcription	Gastric	stomach
3	chr12:121221000-121250000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr12:121221200-121249400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:121221400-121240800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr12:121221600-121238800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr12:121222200-121274000	Weak transcription	Lung	lung
8	chr12:121222400-121238800	Weak transcription	Placenta	Placenta
9	chr12:121222400-121240400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr12:121222600-121249200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr12:121222600-121259000	Weak transcription	Ovary	ovary
12	chr12:121222600-121260800	Weak transcription	Spleen	Spleen
13	chr12:121222600-121268600	Weak transcription	Esophagus	oesophagus
14	chr12:121222600-121268600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr12:121222800-121240600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr12:121222800-121245600	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr12:121222800-121249400	Weak transcription	HSMM	muscle
18	chr12:121228600-121239400	Weak transcription	Liver	Liver
19	chr12:121229000-121245200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:121230000-121239000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr12:121230000-121255200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr12:121231200-121238000	Weak transcription	Left Ventricle	heart
23	chr12:121234000-121240200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:121234000-121240600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr12:121234000-121240800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr12:121234000-121264200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr12:121234200-121246000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr12:121234200-121246000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr12:121234200-121246600	Weak transcription	Fetal Stomach	stomach
30	chr12:121234200-121246800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr12:121234600-121238600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr12:121234600-121238600	Weak transcription	Fetal Lung	lung
33	chr12:121234600-121239000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr12:121234600-121245800	Weak transcription	Fetal Muscle Trunk	muscle
35	chr12:121234600-121246000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr12:121234600-121247200	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr12:121234600-121250600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr12:121234600-121263000	Weak transcription	A549	lung
39	chr12:121234800-121238600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr12:121234800-121245400	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr12:121234800-121246200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr12:121234800-121246600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr12:121234800-121246800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr12:121234800-121250600	Weak transcription	Fetal Brain Female	brain
45	chr12:121235000-121242200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr12:121235000-121246000	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr12:121235000-121249600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr12:121235200-121245200	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr12:121235400-121238000	Flanking Active TSS	GM12878-XiMat	blood
50	chr12:121235600-121237800	Enhancers	Brain Hippocampus Middle	brain

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